Berlin 6 Open Access Conference: Patrick Vandewalle
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1) The document discusses the importance of reproducible research, which refers to the ability of others to accurately replicate experiments and results through access to data, code, and documentation. 2) Examples are provided where sharing implementation code and data helped others understand, build upon, and validate published research in various fields including signal processing. 3) Benefits of reproducible research are outlined, including efficient reuse of one's own work, opportunities for collaboration, and increased impact and understanding of the published research.
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We do cutting edge basic science research to discover the origins of disease and develop new drugs, diagnostics, vaccines and other interventions. Through clinical research, we translate our laboratory discoveries into improved medical treatments. Open access and collaborative research in knowledge societies can have local impacts beyond traditional academic outputs like journal articles. Metrics should recognize development-focused research and scholars working across borders in the global South.
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OpenWetWare is a web-based knowledge sharing resource for biological researchers with the mission of having a meaningful impact on disseminating biological information. It aims to become a premier, open, and lasting environment for biologists to collaborate in real time to produce, share, and improve knowledge. OpenWetWare brings together lab communities, experimental protocols, academic courses, online lab notebooks and other useful information for biological researchers at the speed of the web to accelerate the pace of discovery. It has over 5,000 registered users from around the world who can edit documents to collectively build a system that maps closely to how people in science work openly.
Berlin 6 Open Access Conference: Sergey Fomel
The document discusses reproducible research and outlines steps to achieve it. It describes Jon Claerbout's early work on reproducible research using LaTeX and makefiles at Stanford University. It also discusses the Madagascar project for multidimensional data analysis using open-source tools. Finally, it summarizes several articles from a special issue of CiSE magazine on reproducible computational experiments using tools like R, MATLAB, Python and Fortran.
Berlin 6 Open Access Conference: Philippe Aigrain
Open Access is changing research in three key ways according to the document:
1. Open Access is spreading beyond just publications to include data, protocols, software, research instruments, which is changing the nature of science itself.
2. Open Access is changing the nature of scientific papers by making them accessible to scientists in different fields and advanced users, as well as changing the processes around papers.
3. Open Access is creating new interactions between research and society and moving from just Open Access to publications towards commons-based science where data, protocols, software, and research instruments are also made openly accessible.
Berlin 6 Open Access Conference: Lilia Efimova
This document discusses blogging PhD research and the challenges of managing fragmented bits of research drafts. It touches on using an external repository to store things that don't fit a blog, taking an everyday interactive grounded theory approach, and publishing research in manageable chunks for a real audience. Issues of quality, visibility, attribution and ownership are raised in the context of networked research.
Berlin 6 Open Access Conference: Stefan Weisgerber
International standardization helps maintain long-term accessibility of information. Two standards were developed for document formats - ISO/IEC 26300 for the Open Document Format and ISO/IEC 29500 for the Office Open XML format. While these formats have overlapping functionality, they are not identical. Work is underway to define interoperability between the formats and allow users to choose the best solution.
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Berlin 6 Open Access Conference: Susan Murray (for Eve Gray Murray)
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Berlin 6 Open Access Conference: Stefan Weisgerber
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The document discusses scientific workflows, provenance, and linked data. It covers:
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The document discusses reproducibility in networking research. It summarizes a study on the accessibility of software artifacts from papers presented at SIGCOMM, CoNEXT, and Hotnets conferences between 2013-2014. The study found that only a small portion had their software artifacts publicly available either through a URL in the paper or by contacting the authors. It provides recommendations to improve reproducibility, such as encouraging authors to release source code and data with their papers. The document also discusses challenges around handling and sharing privacy-sensitive network data.
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The document presents a software bug prediction model. It aims to build a resilient bug prediction model through simulation on open source issue trackers like Jira and Bugzilla. It also aims to conduct a comparative study of the new model against existing competitive models. The model will make use of data from software repositories, bug reports, and code artifacts to predict bugs. Open source projects like Eclipse, Mozilla and Android will be used for simulations. Data mining tools like WEKA and RAPID MINER will be utilized extensively. The model also aims to facilitate code refactoring to improve software maintenance activities like modification and enhancement. Literature in the areas of bug prediction and code refactoring will be surveyed. The research will be conducted in
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Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
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The document discusses Microsoft's Cognitive Toolkit (CNTK), an open source deep learning toolkit developed by Microsoft. It provides the following key points:
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This document provides reviews of 3 research papers on distributed systems. The reviews were created by following a structured format including the paper title, authors, main idea, results, impact, evidence, prior work, and ideas for future work. For the first paper, the summary discusses analyzing the cost and resource optimization of running real-life applications on an open source cloud. The second paper proposes a software testing framework called IVRIDIO to provide test-first performance as a cloud service. The third paper presents a formal approach to developing fault tolerant distributed systems using refinement techniques.
MAVRL Workshop 2014 - Python Materials Genomics (pymatgen)
This presentation was part of the workshop on Materials Project Software infrastructure conducted for the Materials Virtual Lab in Nov 10 2014. It presents an introduction to the Python Materials Genomics (pymatgen) materials analysis library. Pymatgen is a robust, open-source Python library for materials analysis. It currently powers the public Materials Project (http://www.materialsproject.org), an initiative to make calculated properties of all known inorganic materials available to materials researchers. These are some of the main features:
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Extensive io capabilities to manipulate many VASP (http://cms.mpi.univie.ac.at/vasp/) and ABINIT (http://www.abinit.org/) input and output files and the crystallographic information file format. This includes generating Structure objects from vasp input and output. There is also support for Gaussian input files and XYZ file for molecules.
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Software tools to facilitate materials science research
The document discusses software tools to facilitate materials science research, noting that the author's group works to standardize and automate computational methods for high-throughput calculations and discovery of new functional materials. It advocates for developing automated workflows and analysis frameworks to reduce errors, improve efficiency, and enable non-experts to easily conduct complex simulations and analyses through intuitive online interfaces. The goal is to make advanced computational materials science accessible to a wider audience.
SyncMeta: Near Real-time Collaborative Conceptual Modeling on the Web
Framework for near real-time (meta) modeling on the Web. Permits the collaborative editing of meta models and the generation of near real-time collaborative modeling editors. It uses a visual modeling approach.
http://dbis.rwth-aachen.de/cms/research/ACIS/SyncMeta
Software tools for high-throughput materials data generation and data mining
Atomate and matminer are open-source Python libraries for high-throughput materials data generation and data mining. Atomate makes it easy to automatically generate large datasets by running standardized computational workflows with different simulation packages. Matminer contains tools for featurizing materials data and integrating it with machine learning algorithms and data visualization methods. Both aim to accelerate materials discovery by automating and standardizing computational workflows and data analysis tasks.
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Illustrated Code: Building Software in a Literate Way
Andreas Zeller, CISPA Helmholtz Center for Information Security
Notebooks – rich, interactive documents that join together code, documentation, and outputs – are all the rage with data scientists. But can they be used for actual software development? In this talk, I share experiences from authoring two interactive textbooks – fuzzingbook.org and debuggingbook.org – and show how notebooks not only serve for exploring and explaining code and data, but also how they can be used as software modules, integrating self-checking documentation, tests, and tutorials all in one place. The resulting software focuses on the essential, is well-documented, highly maintainable, easily extensible, and has a much higher shelf life than the "duct tape and wire” prototypes frequently found in research and beyond.
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Open & reproducible research - What can we do in practice?
- There is a reproducibility crisis in computational research even when code is made available. Out of 206 computational studies in Science magazine since a policy change mandating sharing, only 26 directly provided their code and data. Of those judged potentially reproducible when code was available, more than half still required significant effort to reproduce.
- Making research fully reproducible requires addressing issues like difficult computational environments, long run times, dependency on previous results, and clarity on what is required to reproduce a single finding. Following principles like ensuring code is re-runnable, repeatable, reproducible, reusable, and replicable can help achieve reproducibility. Publishing code on platforms like Zenodo and OSF can also aid reproducibility.
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Results may vary: Collaborations Workshop, Oxford 2014
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From Scientific Workflows to Research Objects: Publication and Abstraction of...
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Software tools to facilitate materials science research
SyncMeta: Near Real-time Collaborative Conceptual Modeling on the Web
SyncMeta: Near Real-time Collaborative Conceptual Modeling on the Web
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Software tools for high-throughput materials data generation and data mining
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Open & reproducible research - What can we do in practice?
More from Cornelius Puschmann
Berlin 6 Open Access Conference: Susan Murray
1. AJOL (African Journals Online) is an online database that provides free access to metadata and full text of African scholarly journals, with the goal of increasing access to and use of African-published research.
2. While AJOL is appreciated for being the largest aggregator of African journals, concerns about quality and evaluation of the journals have been raised.
3. Improving quality, evaluation, and impact assessment of African-published research is important for advancing higher education and development in Africa. Getting more research openly accessible online could help develop new tools to measure research quality and impact.
Berlin 6 Open Access Conference: Julianne Nyhan
The document discusses the European Reference Index for the Humanities (ERIH), which aims to provide a benchmarking tool for comparing humanities research excellence across Europe. It outlines ERIH's objectives, processes, coverage of disciplines and journals. Key points include that ERIH uses peer review to identify high quality journals, has published initial journal lists in 15 disciplines, and is working to update these lists based on feedback. It also discusses open questions around measuring the influence of open access publications in the humanities.
Berlin 6 Open Access Conference: Deirdre Furlong
The document summarizes the European Commission's approach to open access of scientific information in the digital age. It discusses the Commission's role in developing policies at the European level, setting rules as a research funding body through Framework Programmes like FP7, and building capacity through projects. The Commission recognizes the importance of access and dissemination for research and is making steady progress, but more work is still needed, such as monitoring ongoing initiatives and developing policies for FP8.
Berlin 6 Open Access Conference: Dieter Imboden
The document discusses recommendations from EUROHORCs, a European organization of research funding and performing organizations, regarding open access. The recommendations call for scientists to consider open access when publishing research and to self-archive works. They also advise member organizations to sign the Berlin Declaration supporting open access and adopt EURAB recommendations. The document then analyzes financial implications of shifting to more open access models, comparing potential costs to research funders' budgets and publishers' revenues. It raises questions around who will pay for and maintain open access repositories long-term.
Berlin 6 Open Access Conference: Theodore Papazoglou
The document outlines the European Research Council's (ERC) open access policy, which aims to promote the free movement of knowledge within the European research area. The key points of the policy are that peer-reviewed publications and primary research data from ERC-funded projects must be made publicly available through an appropriate open access repository within 6 months of publication. The policy is being implemented through requirements written into the ERC's grant agreements and guidelines for grantees on depositing publications and data in appropriate open access archives and databases.
Berlin 6 Open Access Conference: Gene D. Sprouse
The American Physical Society (APS) is the largest publisher of physics articles and uses a hybrid model of open access and subscriptions. It has 10 publications, including Physical Review Letters and Reviews of Modern Physics. APS allows authors to post final manuscripts online and reuse portions of their work. While subscriptions fund operations, APS is exploring new open access initiatives like SCOAP3 and making more content freely available online at Physics.APS.org. APS believes open access must be sustainable and reversible to subscriptions to ensure the long-term viability of its peer-reviewed journals.
Berlin 6 Open Access Conference: Mark Liberman
The document discusses the history of funding for human language technologies (HLT) research in the US from the 1960s to the present. It describes how funding was halted in the 1960s due to negative reviews of machine translation research. Funding was restarted in 1986 when a DARPA program introduced shared data and evaluation metrics to ensure measurable progress and prevent "glamour and deceit". This common task approach created positive feedback loops and a research culture that drove steady improvements in HLT.
Berlin 6 Open Access Conference: Kai von Fintel
The document discusses ways that the open access journal Semantics & Pragmatics, published by the Linguistic Society of America, aims to go beyond traditional open access models. It publishes peer-reviewed articles in linguistics and also makes available related experimental materials, multimedia components, teaching materials, and ongoing commentary on articles from peer scientists. It considers further expanding this by hosting pre-publication discussion forums for submitted articles concurrent with anonymous peer review.
Berlin 6 Open Access Conference: Christian Zier
Christian Zier of the Federal Office for Information Security in Germany presented on open document exchange formats. He discussed how open standards increase interoperability and security while avoiding vendor lock-in. Zier explained that open document formats like ODF allow complete analysis for security threats and isolation of potentially dangerous code. While ODF meets eGovernment security needs, OOXML has no public implementations and its complexity could reduce interoperability. Zier's office successfully migrated from Microsoft to open solutions like Linux, StarOffice and ODF, with minimal issues.
Berlin 6 Open Access Conference: Frederick Friend
The document discusses what is currently known about the costs and benefits of institutional repositories. More is known about startup costs than ongoing costs, and more about theoretical benefits than practical benefits. It provides examples of repository costs from various studies and outlines factors that affect costs like staffing needs, content type, and potential economies of scale. It also stresses the need to quantify benefits in specific rather than general terms and potentially in financial terms to justify ongoing institutional support. Collecting long-term cost and benefit data tailored to each institution is important for making the case for continued repository funding.
Berlin 6 Open Access Conference: Matthew Cockerill
- Open access publishing business models differ from traditional models in that there are no barriers to access, publishers do not acquire exclusive rights to the content, and are generally paid for publication services rather than through subscriptions.
- Revenue sources for open access publishers include publication fees paid by authors, sponsoring organizations, or member institutions, as well as services like hosting repositories and advertising.
- Publication fees for open access journals typically range from $780-$3000 and cover costs like editorial work, publishing, and marketing that are similar to traditional models. Institutions play a key role in helping fund open access through central funds, memberships, and policies supporting open access publishing.
Berlin 6 Open Access Conference: Salvatore Mele
The document summarizes the SCOAP3 (Sponsoring Consortium for Open Access Publishing in Particle Physics) model, which aims to make scholarly literature in high-energy physics open access by redirecting subscription funds from libraries to publishers. It describes how SCOAP3 would establish a consortium to fund the peer review process for major HEP journals through a tendering process, converting them to open access. It provides updates on SCOAP3's progress in obtaining pledges from countries and highlights related open access developments in HEP publishing.
Berlin 6 Open Access Conference: DK Sahu
This document discusses the benefits of open access publishing for journals from developing countries. It notes that open access increases the visibility and readership of journals globally, helping attract more authors and citations. This in turn can help journals improve quality and get indexed in citation databases. The document also discusses Medknow's open access publishing model, which relies on sources of revenue like print subscriptions, advertisements, membership fees and reprints rather than author fees. Studies of papers published in Medknow journals found that open access significantly increased the number of authors who cited the papers, and that the majority used the open access versions. The document concludes that open access helps journals improve visibility, attract authors, increase quality and research impact without negatively affecting subscriptions.
Berlin 6 Open Access Conference: Arun Arunachalam
- India has made slow progress adopting open access despite opportunities it could provide for scientific advancement and addressing problems like poverty, healthcare, and agriculture. Barriers include a lack of awareness among policymakers and scientists about open access and its advantages.
- Some organizations have begun open access initiatives, like certain CSIR laboratories setting up open access repositories and some scientific journals becoming open access. However, more coordinated efforts are needed across scientific institutions and disciplines.
- Widespread adoption of open access in India could help disseminate knowledge to marginalized communities and support local researchers and health workers in improving conditions. But focused advocacy and training is still required to increase awareness of open access.
Berlin 6 Open Access Conference: Solange dos Santos
1) SciELO is a network of open access scientific electronic libraries that publishes over 500 journals from Latin American, Caribbean, Portuguese, and Spanish-speaking countries.
2) It aims to increase the global visibility and impact of scientific research from developing countries by publishing journals online and providing bibliometric indicators similar to those of other major indexes.
3) Since its launch in 1997, SciELO has expanded to include collections from over a dozen countries and has increased the international visibility, usage, and citations of its published journals.
Berlin 6 Open Access Conference: Lambert Heller
Lambert Heller presented at the Berlin 6 Open Access Conference in Düsseldorf, Germany on November 11-13, 2008. The presentation discussed the rise of blog aggregators as a means of communication within communities and highlighted several examples. It also examined incentives for blogging within scientific communities and tensions between emerging practices of open development and acknowledgment from academic institutions. The presentation argued that publishers, funders, and other groups need to recognize the impact of blogging and adapt their strategies accordingly.
Berlin 6 Open Access Conference: Tony Hey
The document discusses how data-centric science is driving the need for new tools and technologies to support large-scale data sharing and collaboration. It provides examples of projects like the Sloan Digital Sky Survey that have pioneered new models for open data publishing and public engagement with science. Microsoft research is working on technologies to support the entire scientific research lifecycle from data acquisition and modeling to analysis, visualization, and open dissemination of research outputs.
Berlin 6 Open Access Conference: Wolfram Horstmann
This document discusses open access (OA) in scholarly communication and the relationship between OA, information and communication technology (ICT), and policy. It notes that while OA has spread as a concept, significant challenges remain regarding global copyright, infrastructure development, and coordination between stakeholders. The document suggests two views on advancing OA - focusing first on added-value services for scholars or first on developing global ICT infrastructure through joint efforts of technical and policy groups.
More from Cornelius Puschmann (20)
Berlin 6 Open Access Conference: Theodore Papazoglou
Berlin 6 Open Access Conference: Theodore Papazoglou
Berlin 6 Open Access Conference: Matthew Cockerill
Berlin 6 Open Access Conference: Matthew Cockerill
Berlin 6 Open Access Conference: Solange dos Santos
Berlin 6 Open Access Conference: Solange dos Santos
Berlin 6 Open Access Conference: Wolfram Horstmann
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ANATOMY AND BIOMECHANICS OF HIP JOINT.pdf
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
Mule event processing models | MuleSoft Mysore Meetup #47
Mule event processing models | MuleSoft Mysore Meetup #47
Event Link:- https://meetups.mulesoft.com/events/details/mulesoft-mysore-presents-mule-event-processing-models/
Agenda
● What is event processing in MuleSoft?
● Types of event processing models in Mule 4
● Distinction between the reactive, parallel, blocking & non-blocking processing
For Upcoming Meetups Join Mysore Meetup Group - https://meetups.mulesoft.com/mysore/YouTube:- youtube.com/@mulesoftmysore
Mysore WhatsApp group:- https://chat.whatsapp.com/EhqtHtCC75vCAX7gaO842N
Speaker:-
Shivani Yasaswi - https://www.linkedin.com/in/shivaniyasaswi/
Organizers:-
Shubham Chaurasia - https://www.linkedin.com/in/shubhamchaurasia1/
Giridhar Meka - https://www.linkedin.com/in/giridharmeka
Priya Shaw - https://www.linkedin.com/in/priya-shaw
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Berlin 6 Open Access Conference: Patrick Vandewalle
- 1. Experiences with Reproducible Research in Various Facets of Signal Processing Research Patrick Vandewalle Philips Research, The Netherlands November 12, 2008
- 3. Berlin 6 Conference - Introduction Some examples: “ I just read your paper X. It is very completely described, however I am confused by Y. Could you provide the implementation code to me for reference if possible?” “ Comment from a reviewer about a paper: Please replace Figure 3 by a higher quality version. Also, the horizontal axis should be labeled ‘t’ instead of ‘x’.” “ Hi! I am also working on a project related to X. I have implemented your algorithm, but cannot get the same results as described in your paper. Which values should I use for parameters Y and Z?”